Reliable RT‐PCR detection of Apple stem pitting virus in pome fruits and its association with quince fruit deformation disease

In this study a spot nested RT‐PCR assay was developed for the detection of Apple stem pitting virus (ASPV). A one step RT‐PCR for the generic detection of foveaviruses using degenerate primers that target a conserved region of the RNA‐dependent RNA polymerase (RdRp) gene was followed by a nested PCR that amplifies a 312 bp ASPV specific product. The method is rapid, simple and displays high sensitivity and broad detection range, overcoming the virus molecular variability. The optimum sampling conditions for reliable virus detection were also investigated. ASPV was detected throughout the year in different plant tissues of affected trees, thus the method could be used for routine screening and in certification schemes of pome fruits. ASPV was detected in quince orchards in Greece in all trees that were tested, showing a fruit deformation disorder. Sequencing and phylogenetic analysis of amplicons generated by RT‐PCR from plant tissue affected with the deformation disease indicated that the agent responsible was a variant of ASPV.